It sounds like 3 distinct problems: a CC isn’t being sent, noise when powering the MC6, and noise when MC6 is powering itself.
CC
There shouldn’t be any difference between Host and Device mode, the paths are the same on the MetaModule. I would probably try to track down why that one CC is not getting sent by making a new patch, adding any module, and then start to create a new MIDI mapping to one of the module’s knobs. In that pop-up you will see what MIDI message the MetaModule is receiving. Perhaps the MC6 is sending it over some different channel or doing something else unexpected.
Device mode is pretty new in the firmware, so it’s possible we’re seeing some bug in the firmware but it’d be strange for it to just filter one CC. Try changing the CC number, the MIDI channel, try other MIDI signals and see what gets through. I’m able to get CCs on all channels, when sending from VCV Rack on my computer. Try that and make sure the CC + channel you’re expecting can make it from a different source.
Powering the MC6 with the MetaModule
As for the noise when you’re using the MetaModule to power the MC6, is the MC6 connected to anything else besides the MetaModule? I would suspect ground loops if so. If not, then if it were on my bench I would poke around the power supply rails. I looked at the specs and the unit draws 330mA (or more if other thing are connected to it). That’s on the high side, though safe because the MM can supply 500mA. Ultimately the USB VBUS 5V is generated from the +12V rail, it’s possible the increased load on the rails is causing noise somewhere.
If you have access to a scope you could probably probe the +5V USB supply (I can show you where to probe), and the +12V eurorack power supply rails to see where the noise is coming from. The power supply for the audio path on the MetaModule is completely separate from the USB VBUS supply, so it’s unlikely a taxed VBUS would bleed over to the audio, I would think some sort of ground issue is more likely, but these kinds of issues can be complex. Keep in mind whatever’s powering your speakers and mixer any other gear in the signal path is also part of the equation.
If you happen to have a battery powered headphone amp, plugging that into the MetaModule’s output and listening for noise will tell you something.
Separate power supply for the MC6
As for when you power the MC6 with its own power supply, and connect the MetaModule in Host mode, if the MC6 is USB-compliant then the MetaModule will not turn on VBUS. I’ve seen one non-compliant self-powered USB device (from a well-respected, major manufacturer) that does something scary: it requests VBUS power from the Host, and then physically connects the incoming VBUS to its own internal 5V power supply. So two power supplies are feeding into each other and battling it out. Hopefully the MC6 doesn’t do this! But if it does, then that’s your noise right there.